These are very slow on large networks. get_blog_count() and get_user_count() would mitigate this somewhat, although they too can cause problem on large networks.

Perhaps users.php and sites.php should consult get_user_count() and get_blog_count() and not do a query if the count is over a certain threshold. The tables would default to being empty and a search would have to be performed to get results.

Further, a large network flag may be needed so that functions like get_blog_count() and get_user_count() can avoid ever running COUNT queries and instead rely on the network admin to perform counts and populate the count site options via a separate job.